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Molecular Docking Analysis Central JSM Chemistry Bringing Excellence in Open Access Research Article *Corresponding author Rakesh Kumar Sharma, Department of CBRN defense, Institute of Nuclear Medicine and Allied Sciences, Molecular Docking Analysis - An Delhi-110054, India, Tel: 0091-11-23968900; Fax: 91-11- 23919509; Email: Submitted: 09 March 2016 aid for Selection of Promising Accepted: 31 March 2016 Published: 02 April 2016 Natural Plant Products against ISSN: 2333-6633 Copyright Diphtheria Toxin © 2016 Sharma et al. OPEN ACCESS Ankita Singh Chakotiya, Raman Chawla, Ankit Tanwar, Anamika Sharma and Rakesh Kumar Sharma* Keywords Department of CBRN defense, Institute of Nuclear Medicine and Allied Sciences, India • Corynebacterium diphtheriae • Diphtheria toxin • Natural plant products Abstract • Molecular docking • Lipinski rule of five Molecular docking study was performed in order to identify Natural Plant Products that shows higher binding energy with Diphtheria toxin of the pathogen Corynebacterium diphtheriae, responsible for Diphtheria, a respiratory tract infection. Thirty herbals were selected based on their ethnopharmacological activities reported against different clinical problems. Five phytoconstituents from each herbal were docked with the tertiary chemical structure of Diphtheria toxin and compared with the binding potential obtained from substrate of the toxin, i.e., Nicotinamide adenine dinucleotide. Further, the potent Natural Plant Products were screened for compliance to the Lipinski rule of five with molinspiration tool. It was found that 20 Natural Plant Products from 14 herbals have shown E-value lower than Nicotinamide adenine dinucleotide. Only 03 phytoconstituents Cyanidin (Sambucus nigra), 3-hydroxyflavanone (Oxycoccus palustris) and 6-gingerol (Zingiber officinale) have shown no violation from Lipinski’s rule of five. ABBREVIATIONS it an endemic in such geographical regions [6]. India, a South East Asian country, is considered as the hot zone of Diphtheria DT: Diphtheria Toxin; WHO: World Health Organization; EF-2: Elongation Factor- 2; NAD: Nicotinamide Adenine Dinucleotide; recorded ADPR: Adenosine Diphosphate Ribose; NPPs: Natural Plant Alsoinfection an outbreak with more of Diphtheria than 6,000 is recorded cases (~ by 83.51% Integrated morbidity) Disease Products; SPF: Spherical Polar Fourier; MMDB: Molecular as per the disease surveillance report of WHO, 2015 [7]. implementation of Expanded Programme on Immunization (EPI) Entry System; PDB: Protein Data Bank Surveillance Programme in India in 2014 [8]. However, after the Modeling Database; SMILES: Simplified Molecular-Input Line- INTRODUCTION C. diphtheriae anti-infectionby WHO in 1984, agents, significant i.e., penicillin decline and was erythromycin observed in morbidity[6]. Other Diphtheria, a serious malady caused by Corynebacterium alternative[7]. second isline known chemotherapeutic to be vulnerable modalities to the first include line diphtheriae, has been known to cause intense respiratory amoxicillin, vancomycin, clindamycin, tetracycline, rifampin, disease attributed towards its high transmissibility and toxin kanamycin, gentamycin, imipenem, etc. These antibiotics are intervention(s) [1-3]. The infection is predominantly portrayed acting differently on physiological pathways and molecular by the formation of a pseudo-membrane over tonsils and pharynx, mechanism of the bacteria, but none of them is targeting the DT, which is one of the major virulent factors to cause death of the pseudo-membrane leads to dyspnoea [1]. The condition becomes host cell ultimately reaching up to trachea. Subsequent inflammation of more serious when the toxigenic strains produce DT that is by inactivating EF-2 during chain elongation process of protein absorbed in circulation and ultimately affect many tissues [1,4]. synthesis.[9]. DT DTact inhibitscatalytically protein by utilizingsynthesis NAD of eukaryoticfor transferring cells The main challenge in clinical management of Diphtheria is the ADPR moiety from NAD to EF-2, thereby inactivating EF-2 and limited prognostic as well as therapeutic interventions. However, ultimately kills susceptible cell can prevent the action of DT at mechanistic level and ultimately inhibit the inactivation of EF-2 needs[9]. Therefore, to be explored. the agent Hence that in the death rate significantly declined after the introduction of nations with temperate environment are conducive for the easy the present study rationale based molecular docking approach is growthfirst line and Diphtheria dissemination antitoxin of C.in diphtheriaethe early ,1940’s thereby [5]. making Asian employed to identify potent NPPs that can bind more efficiently Cite this article: Chakotiya AS, Chawla R, Tanwar A, Sharma A, Sharma RK (2016) Molecular Docking Analysis - An aid for Selection of Promising Natural Plant Products against Diphtheria Toxin. JSM Chem 4(1): 1017. Sharma et al. (2016) Email: Central Bringing Excellence in Open Access with DT. The basis of this molecular docking analysis is evaluation RESULTS AND DISCUSSION of minimization of binding energy that is obtained by the correct Molecular Docking: The tertiary structure of Diphtheria toxin conformation of the complex analyzed by using SPF correlation. Results obtained from the present study need further validation at both in vitro and preclinical levels. herbals(with PDB were and docked MMDB with ID asDiphtheria 1SGK and toxin 57365, using respectively) Hex 6.12. It was MATERIALS AND METHODS retrieved from MMDB database. The predominant NPPs of 30 Receptor Kcal/mol)found that (Table20 phytoconstituents 1). of different categories from 14 herbals have shown lower E-value as compared to NAD (-300.05 The ligands were also checked for conformity to the Lipinski taken from MMDB (http://www.ncbi.nlm.nih.gov). The three dimensional crystal structure of receptor ‘DT’ was Ligands rule states that a molecule likely to be developed as an orally activerule of drug five, candidateand the results should are show summarized no more than in (Table one violation 2). The of the following four criteria: (i) It should not have more than and its substrate NAD were taken as ligands. The structural dataOne format hundred of ligands and fifty (NPPs NPPs fromand NAD)30 herbals was (~5obtained from each)from PubChem and converted into SMILES formula by using Open five hydrogen bond donors, (ii) it should not have more than Babel Graphical user interface program (http://openbabel.org/ 10 hydrogen bond acceptors, (iii) it should not have molecular propertiesweight greater of allthan NPPs 500 wereDa, and calculated (iv) it shouldby molinspiration, not have an ligands were attained by online SMILES translator and structure octanol–water partition coefficient greater than 5. Molecular generatordocs/dev/GUI/GUI.html) (http://cactus.nci.nih.gov/translate/). [10, 11]. The PDB file formats of all (Sambucus nigra Oxycoccus palustris) and 6-gingeroland it was ( found that 03 phytoconstituents) have a good potential namely for Cyanidineventual Molecular Docking: Molecular simulation was performed Zingiber officinale development as ),oral 3-hydroxyflavanone agents and can be ( potentially active drug candidates. and ligand. The parameters involved were shape + electro by using Hex 6.12 with PDB file pattern filter for both receptor DISCUSSION receptor and ligand to calculate the linear relationship based complementarity, 1 grid dimension and 180° range angle of The objective of this study was to identify the NPPs that can bindingVirtual energy screening of receptor-ligand of leads: The complexlead molecules [10, 11]. were screened of DT. Many studies are ongoing for the discovery of novel drug inbind order efficiently to mana withge DTdiphtheria in comparison based to on that various of NAD, therapeutic substrate rationale therapies. Discovery of antibiotics and anti-toxin is for drug likeliness on the basis of “Lipinski’s Rule of Five” by usingTable Molinspiration1: Cheminformatics 2016. S. No.E-value of ligandsPhytoconstituents < -300.05 Kcal/mol (NAD). Herbal Class E vale(Kcal/mol) 1. Crocin Gardenia jasminoide Carotenoid 2. Nimbin Azadiracta indica Alkaloid -391.27 3. Azadirachtin Azadiracta indica Limnoid -407.89 4. Vicenin Ocimum sanctum Flavanoid glycoside -429.03 Eriocitrin Mentha piperita Flavanone -490.87 5.6. Beta carotene Solanum lycopersicum Terpenoids -319.75 Betulinic acid Syzigium cumunii Terpenoids -359.57 7. Ecdysterone Achyranthes aspera Sterol -300.89 8. Furosin Emblica officinalis Tannin -317.97 9. Hesperidine Citrus limonum Flavanone -475.19 10.11. Oxycoccus palustris Flavanone -471.63 12. 3-Cycloeucalenol hydroxyflavone Tabermontana coronaria Terpenoid -304.83 13. Lupeol acetate Tabermontana coronaria Terpenoid -396.77 14. Stigmasterol Tabermontana coronaria Sterol -450.22 Viminalol Tabermontana coronaria Terpene -433.50 16.15. 6-gingerol Zingiber officinale Alkaloid -418.19 Beta-farnasene Zingiber officinale Terpene -357.77 17. Zingiberene Zingiber officinale Terpene -303.12 18. Spirostanol Tribulus terrestris Saponin -309.76 19. Cyanidin Sambucus nigra Flavanoid -420.3 20. -329.92 JSM Chem 4(1): 1017 (2016) 2/4 Sharma et al. (2016) Email: Central Bringing Excellence in Open Access Table 2: Molinspiration Calculation of Properties for the Lipinski Rule of Five. Three NPPs (shown in bold) are drug able moieties. S.No. Phytoconstituents n violation n atoms milogP <5 MW <500 nOH <10 nOHNH <5 nrotb 1. Cyanidin 0 21 -0.75 287.25 6 5 1 2. 3- hydroxylflavone 0 38 3.45 238.24 3 1 1 3. 6-gingerol 0 21 3.22 294.39 4 2 10 4. Betulinic acid 1 33 3 2 2 Nimbin 1 7.04 456.71 5.6. Ecdysterone 1 3934 1.363.55 540.61 9 06 8 Cycloeucalenol 1 31 480.64 71 1 5 7. Lupeol acetate 1 34 7.62 426.73 2 35 8. Stigmasterol 1 8.71 468.77 1 01 9. Viminalol 1 3031 7.87 412.70 1 1 5 10.11. Beta-farnasene 1 8.08 426.73 0 12. Zingiberene 1 15 5.84 204.36 0 0 74 13. Spirostanol 1 15 5.126.12 204.36 03 10 14. Beta-carotene 2 30 416.65 0 Azadirachtin 2 40 9.841.42 536.89 160 03 10 15.16. Eriocitrin 3 51 720.72 14 104 Hesperidine 3 4043 -1.68 564.60 10 17. Furosin 3 46 -0.55 234.30 15 8 47 18. Vicenin 3 --1.62 2.56 650.45 1914 10 4 19.
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